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Yorodumi- PDB-2w55: Crystal Structure of Xanthine Dehydrogenase (E232Q variant) from ... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2w55 | ||||||
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| Title | Crystal Structure of Xanthine Dehydrogenase (E232Q variant) from Rhodobacter capsulatus in Complex with Hypoxanthine | ||||||
Components | (XANTHINE DEHYDROGENASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / XDH / GOUT / IRON / XANTHINE / IRON-SULFUR / MOLYBDENUM COFACTOR / HYPOXANTHINE / METAL-BINDING | ||||||
| Function / homology | Function and homology information1.1.1.204 / xanthine dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding Similarity search - Function | ||||||
| Biological species | RHODOBACTER CAPSULATUS (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Doebbler, J.A. / Truglio, J.J. / Leimkuhler, S. / Kisker, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009Title: Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase. Authors: Dietzel, U. / Kuper, J. / Doebbler, J.A. / Schulte, A. / Truglio, J.J. / Leimkuhler, S. / Kisker, C. | ||||||
| History |
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| Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2w55.cif.gz | 876.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2w55.ent.gz | 706 KB | Display | PDB format |
| PDBx/mmJSON format | 2w55.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2w55_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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| Full document | 2w55_full_validation.pdf.gz | 2.9 MB | Display | |
| Data in XML | 2w55_validation.xml.gz | 164.2 KB | Display | |
| Data in CIF | 2w55_validation.cif.gz | 219.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w55 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w55 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2w3rC ![]() 2w3sC ![]() 2w54C ![]() 1jroS C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
NCS oper:
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Components
-Protein , 2 types, 8 molecules ACEGBDFH
| #1: Protein | Mass: 49420.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ![]() #2: Protein | Mass: 82977.047 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ![]() |
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-Non-polymers , 6 types, 67 molecules 










| #3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-XAX / {[( #6: Chemical | ChemComp-BA / #7: Chemical | ChemComp-HPA / #8: Water | ChemComp-HOH / | |
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-Details
| Compound details | ENGINEERED RESIDUE IN CHAIN B, GLU 232 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLU 232 TO GLN ...ENGINEERED |
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| Sequence details | E232Q VARIANT |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.25 % / Description: NONE |
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| Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.3 Details: 100 MM TRIS PH 8.3, 6-8 % PEG 8000, 6-8 MM BACL, 5-25 MM DTT, 3-4 % ISOPROPANOL, 10-15 MG/ML PROTEIN IN A 1:2 RATIO WITH THE RESERVOIR SOLUTION, HANGING DROP VAPOR DIFFUSION |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 |
| Detector | Type: ADSC CCD / Detector: CCD / Details: A DOUBLY FOCUSING TOROIDAL MIRROR |
| Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 3.4→50 Å / Num. obs: 83695 / % possible obs: 93.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.8 |
| Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 69 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1JRO Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.841 / SU B: 64.606 / SU ML: 0.48 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.633 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 43.12 Å2
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| Refinement step | Cycle: LAST / Resolution: 3.4→50 Å
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| Refine LS restraints |
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RHODOBACTER CAPSULATUS (bacteria)
X-RAY DIFFRACTION
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